X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ba554bbf8076caae0928b426e640f6660ee9e068..a54c0f72656d883ae8f27d5074e35f60e61dce09:/sdk/cwl/tests/test_submit.py

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index b44f6feb5d..f828347019 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -42,7 +42,7 @@ import arvados.keep
 from .matcher import JsonDiffMatcher, StripYAMLComments
 from .mock_discovery import get_rootDesc
 
-import ruamel.yaml as yaml
+import ruamel.yaml
 
 _rootDesc = None
 
@@ -69,7 +69,9 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
 
             uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
                                  "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
-                                 "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
+                                 "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5",
+                                 "df80736f-f14d-4b10-b2e3-03aa27f034b6", "df80736f-f14d-4b10-b2e3-03aa27f034b7",
+                                 "df80736f-f14d-4b10-b2e3-03aa27f034b8", "df80736f-f14d-4b10-b2e3-03aa27f034b9"]
 
             determine_image_id.return_value = None
 
@@ -179,12 +181,6 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
             stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
             stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
 
-            stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
-            stubs.api.jobs().create().execute.return_value = {
-                "uuid": stubs.expect_job_uuid,
-                "state": "Queued",
-            }
-
             stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
             stubs.api.container_requests().create().execute.return_value = {
                 "uuid": stubs.expect_container_request_uuid,
@@ -192,96 +188,11 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
                 "state": "Queued"
             }
 
-            stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
-            stubs.api.pipeline_templates().create().execute.return_value = {
-                "uuid": stubs.expect_pipeline_template_uuid,
-            }
-            stubs.expect_job_spec = {
-                'runtime_constraints': {
-                    'docker_image': '999999999999999999999999999999d3+99',
-                    'min_ram_mb_per_node': 1024
-                },
-                'script_parameters': {
-                    'x': {
-                        'basename': 'blorp.txt',
-                        'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
-                        'class': 'File'
-                    },
-                    'y': {
-                        'basename': '99999999999999999999999999999998+99',
-                        'location': 'keep:99999999999999999999999999999998+99',
-                        'class': 'Directory'
-                    },
-                    'z': {
-                        'basename': 'anonymous',
-                        "listing": [{
-                            "basename": "renamed.txt",
-                            "class": "File",
-                            "location": "keep:99999999999999999999999999999998+99/file1.txt",
-                            "size": 0
-                        }],
-                        'class': 'Directory'
-                    },
-                    'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
-                },
-                'repository': 'arvados',
-                'script_version': 'master',
-                'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
-                'script': 'cwl-runner'
-            }
-            stubs.pipeline_component = stubs.expect_job_spec.copy()
-            stubs.expect_pipeline_instance = {
-                'name': 'submit_wf.cwl',
-                'state': 'RunningOnServer',
-                'owner_uuid': None,
-                "components": {
-                    "cwl-runner": {
-                        'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
-                        'script_parameters': {
-                            'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
-                            'x': {"value": {
-                                'basename': 'blorp.txt',
-                                'class': 'File',
-                                'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
-                                "size": 16
-                            }},
-                            'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
-                                  'listing': [
-                                      {
-                                          'basename': 'renamed.txt',
-                                          'class': 'File', 'location':
-                                          'keep:99999999999999999999999999999998+99/file1.txt',
-                                          'size': 0
-                                      }
-                                  ]}},
-                            'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
-                            'arv:debug': True,
-                            'arv:enable_reuse': True,
-                            'arv:on_error': 'continue'
-                        },
-                        'repository': 'arvados',
-                        'script_version': 'master',
-                        'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
-                        'script': 'cwl-runner',
-                        'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
-                    }
-                }
-            }
-            stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
-            stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
-            stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
-            stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
-            stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
-                "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
-                "state": "Queued"
-            }
-            stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
-            stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
-
             cwd = os.getcwd()
-            filepath = os.path.join(cwd, "tests/wf/submit_wf_packed.cwl")
+            filepath = os.path.join(cwd, "tests/wf/submit_wf_wrapper.cwl")
             with open(filepath) as f:
-                expect_packed_workflow = yaml.round_trip_load(f)
+                yaml = ruamel.yaml.YAML(typ='rt', pure=True)
+                expect_packed_workflow = yaml.load(f)
 
             if wfpath is None:
                 wfpath = wfname
@@ -290,16 +201,20 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
             gitinfo_workflow["$graph"][0]["id"] = "file://%s/tests/wf/%s" % (cwd, wfpath)
             mocktool = mock.NonCallableMock(tool=gitinfo_workflow["$graph"][0], metadata=gitinfo_workflow)
 
-            git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
-            expect_packed_workflow.update(git_info)
+            stubs.git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
+            expect_packed_workflow.update(stubs.git_info)
 
-            git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in git_info.items()}
+            stubs.git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in stubs.git_info.items()}
 
+            step_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
             if wfname == wfpath:
-                container_name = "%s (%s)" % (wfpath, git_props["arv:gitDescribe"])
+                container_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
             else:
                 container_name = wfname
 
+            expect_packed_workflow["$graph"][0]["steps"][0]["id"] = "#main/"+step_name
+            expect_packed_workflow["$graph"][0]["steps"][0]["label"] = container_name
+
             stubs.expect_container_spec = {
                 'priority': 500,
                 'mounts': {
@@ -358,8 +273,8 @@ def stubs(wfdetails=('submit_wf.cwl', None)):
                     'vcpus': 1,
                     'ram': (1024+256)*1024*1024
                 },
+                'properties': stubs.git_props,
                 'use_existing': False,
-                'properties': git_props,
                 'secret_mounts': {}
             }
 
@@ -383,7 +298,7 @@ class TestSubmit(unittest.TestCase):
 
     def setUp(self):
         cwltool.process._names = set()
-        arvados_cwl.arvdocker.arv_docker_clear_cache()
+        #arvados_cwl.arvdocker.arv_docker_clear_cache()
 
     def tearDown(self):
         root_logger = logging.getLogger('')
@@ -393,7 +308,7 @@ class TestSubmit(unittest.TestCase):
         root_logger.handlers = handlers
 
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_invalid_runner_ram(self, stubs, tm):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
@@ -402,7 +317,7 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 1)
 
 
-    @stubs
+    @stubs()
     def test_submit_container(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
@@ -414,7 +329,7 @@ class TestSubmit(unittest.TestCase):
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
                 'replication_desired': None,
-                'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+                'name': 'submit_wf.cwl ('+ stubs.git_props["arv:gitDescribe"] +') input (169f39d466a5438ac4a90e779bf750c7+53)',
             }), ensure_unique_name=False),
             mock.call(body=JsonDiffMatcher({
                 'manifest_text':
@@ -432,7 +347,7 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_submit_container_tool(self, stubs):
         # test for issue #16139
         exited = arvados_cwl.main(
@@ -444,7 +359,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_no_reuse(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
@@ -457,7 +372,7 @@ class TestSubmit(unittest.TestCase):
             '--no-log-timestamps', '--disable-validate', '--disable-color',
             '--eval-timeout=20', '--thread-count=0',
             '--disable-reuse', "--collection-cache-size=256",
-            "--output-name=Output from workflow submit_wf.cwl",
+            '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
             '--debug', '--on-error=continue',
             '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
         expect_container["use_existing"] = False
@@ -479,16 +394,17 @@ class TestSubmit(unittest.TestCase):
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         expect_container["command"] = ["--disable-reuse" if v == "--enable-reuse" else v for v in expect_container["command"]]
         expect_container["use_existing"] = False
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
             {
-                "class": "http://arvados.org/cwl#ReuseRequirement",
+                "class": "WorkReuse",
                 "enableReuse": False,
             },
+                {
+                    "acrContainerImage": "999999999999999999999999999999d3+99",
+                    "class": "http://arvados.org/cwl#WorkflowRunnerResources"
+                }
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
-            "arv": "http://arvados.org/cwl#",
-            "cwltool": "http://commonwl.org/cwltool#"
-        }
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:fa5fbf21deb74f9f239daa3f5bb4b902+292/wf/submit_wf_no_reuse.cwl"
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -496,7 +412,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
 
 
-    @stubs
+    @stubs()
     def test_submit_container_on_error(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
@@ -508,7 +424,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=stop',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -518,7 +434,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_output_name(self, stubs):
         output_name = "test_output_name"
 
@@ -542,7 +458,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_storage_classes(self, stubs):
         exited = arvados_cwl.main(
             ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
@@ -554,7 +470,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       '--output-name=Output from workflow submit_wf.cwl',
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        "--debug",
                                        "--storage-classes=foo", '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -565,7 +481,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_multiple_storage_classes(self, stubs):
         exited = arvados_cwl.main(
             ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
@@ -577,7 +493,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        "--debug",
                                        "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -591,7 +507,7 @@ class TestSubmit(unittest.TestCase):
     @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
-    @stubs
+    @stubs()
     def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
         final_output_c = arvados.collection.Collection()
         make_output.return_value = ({},final_output_c)
@@ -602,17 +518,17 @@ class TestSubmit(unittest.TestCase):
         job.side_effect = set_final_output
 
         exited = arvados_cwl.main(
-            ["--debug", "--local", "--storage-classes=foo",
+            ["--debug", "--local", "--storage-classes=foo", "--disable-git",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
+        make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
         self.assertEqual(exited, 0)
 
     @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
-    @stubs
+    @stubs()
     def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
         final_output_c = arvados.collection.Collection()
         make_output.return_value = ({},final_output_c)
@@ -624,17 +540,17 @@ class TestSubmit(unittest.TestCase):
         job.side_effect = set_final_output
 
         exited = arvados_cwl.main(
-            ["--debug", "--local",
+            ["--debug", "--local", "--disable-git",
                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
+        make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
         self.assertEqual(exited, 0)
 
     @mock.patch("cwltool.task_queue.TaskQueue")
     @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
     @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
-    @stubs
+    @stubs()
     def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
         final_output_c = arvados.collection.Collection()
         make_output.return_value = ({},final_output_c)
@@ -645,14 +561,14 @@ class TestSubmit(unittest.TestCase):
         job.side_effect = set_final_output
 
         exited = arvados_cwl.main(
-            ["--debug", "--local",
+            ["--debug", "--local", "--disable-git",
                 "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
-        make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
+        make_output.assert_called_with(u'Output from workflow submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_output_ttl(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
@@ -664,7 +580,8 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl", '--debug',
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug',
                                        '--on-error=continue',
                                        "--intermediate-output-ttl=3600",
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -675,7 +592,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_trash_intermediate(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
@@ -688,6 +605,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        "--trash-intermediate",
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -698,7 +616,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_output_tags(self, stubs):
         output_tags = "tag0,tag1,tag2"
 
@@ -712,7 +630,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        "--output-tags="+output_tags, '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -722,7 +640,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_runner_ram(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
@@ -731,6 +649,13 @@ class TestSubmit(unittest.TestCase):
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
+                {
+                    "acrContainerImage": "999999999999999999999999999999d3+99",
+                    "class": "http://arvados.org/cwl#WorkflowRunnerResources",
+                    "ramMin": 2048
+                }
+        ]
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -740,7 +665,7 @@ class TestSubmit(unittest.TestCase):
 
     @mock.patch("arvados.collection.CollectionReader")
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_file_keepref(self, stubs, tm, collectionReader):
         collectionReader().exists.return_value = True
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
@@ -752,7 +677,7 @@ class TestSubmit(unittest.TestCase):
 
     @mock.patch("arvados.collection.CollectionReader")
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_keepref(self, stubs, tm, reader):
         with open("tests/wf/expect_arvworkflow.cwl") as f:
             reader().open().__enter__().read.return_value = f.read()
@@ -813,13 +738,13 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 0)
 
     @mock.patch("time.sleep")
-    @stubs
+    @stubs()
     def test_submit_arvworkflow(self, stubs, tm):
         with open("tests/wf/expect_arvworkflow.cwl") as f:
             stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
 
         exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--api=containers", "--debug",
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git",
              "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -838,6 +763,7 @@ class TestSubmit(unittest.TestCase):
                     'kind': 'json',
                     'content': {
                         'cwlVersion': 'v1.0',
+                        'label': 'a test workflow',
                         '$graph': [
                             {
                                 'id': '#main',
@@ -863,8 +789,7 @@ class TestSubmit(unittest.TestCase):
                                 'requirements': [
                                     {
                                         'dockerPull': 'debian:buster-slim',
-                                        'class': 'DockerRequirement',
-                                        "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
+                                        'class': 'DockerRequirement'
                                     }
                                 ],
                                 'id': '#submit_tool.cwl',
@@ -888,8 +813,11 @@ class TestSubmit(unittest.TestCase):
             'command': ['arvados-cwl-runner', '--local', '--api=containers',
                         '--no-log-timestamps', '--disable-validate', '--disable-color',
                         '--eval-timeout=20', '--thread-count=0',
-                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                        '--enable-reuse', "--collection-cache-size=256",
+                        "--output-name=Output from workflow a test workflow",
+                        '--debug', '--on-error=continue',
                         '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+            'output_name': 'Output from workflow a test workflow',
             'cwd': '/var/spool/cwl',
             'runtime_constraints': {
                 'API': True,
@@ -924,7 +852,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_missing_input(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
@@ -938,7 +866,7 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
         self.assertEqual(exited, 1)
 
-    @stubs
+    @stubs()
     def test_submit_container_project(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -953,7 +881,8 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        "--eval-timeout=20", "--thread-count=0",
                                        '--enable-reuse', "--collection-cache-size=256",
-                                       "--output-name=Output from workflow submit_wf.cwl", '--debug',
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug',
                                        '--on-error=continue',
                                        '--project-uuid='+project_uuid,
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@@ -964,7 +893,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_eval_timeout(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
@@ -976,6 +905,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=60.0', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -985,7 +915,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_collection_cache(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
@@ -997,6 +927,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=0',
                                        '--enable-reuse', "--collection-cache-size=500",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
         expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
@@ -1007,7 +938,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_thread_count(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
@@ -1019,6 +950,7 @@ class TestSubmit(unittest.TestCase):
                                        '--no-log-timestamps', '--disable-validate', '--disable-color',
                                        '--eval-timeout=20', '--thread-count=20',
                                        '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
                                        '--debug', '--on-error=continue',
                                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
@@ -1028,7 +960,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_runner_image(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
@@ -1036,6 +968,12 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
         stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
+        stubs.expect_container_spec["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
+                {
+                    "acrContainerImage": "999999999999999999999999999999d5+99",
+                    "class": "http://arvados.org/cwl#WorkflowRunnerResources"
+                }
+        ]
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         stubs.api.container_requests().create.assert_called_with(
@@ -1044,7 +982,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_priority(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
@@ -1073,18 +1011,20 @@ class TestSubmit(unittest.TestCase):
             "vcpus": 2,
             "ram": (2000+512) * 2**20
         }
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
             {
                 "class": "http://arvados.org/cwl#WorkflowRunnerResources",
+                "acrContainerImage": "999999999999999999999999999999d3+99",
                 "coresMin": 2,
                 "ramMin": 2000,
                 "keep_cache": 512
             }
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
-            "arv": "http://arvados.org/cwl#",
-        }
+        #expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
+        #    "arv": "http://arvados.org/cwl#",
+        #}
         expect_container["command"] = ["--collection-cache-size=512" if v == "--collection-cache-size=256" else v for v in expect_container["command"]]
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:80b60e39456505b91d3989a1f5058b98+308/wf/submit_wf_runner_resources.cwl"
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -1096,7 +1036,7 @@ class TestSubmit(unittest.TestCase):
     @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
     @mock.patch("arvados.api")
     def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
-        arvados_cwl.arvdocker.arv_docker_clear_cache()
+        #arvados_cwl.arvdocker.arv_docker_clear_cache()
 
         arvrunner = mock.MagicMock()
         arvrunner.project_uuid = ""
@@ -1148,13 +1088,16 @@ class TestSubmit(unittest.TestCase):
                          arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext))
 
 
-    @stubs
+    @stubs()
     def test_submit_secrets(self, stubs):
         exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--api=containers", "--debug",
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git",
                 "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
 
+        stubs.git_props["arv:gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+        stubs.git_info["http://arvados.org/cwl#gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+
         expect_container = {
             "command": [
                 "arvados-cwl-runner",
@@ -1167,8 +1110,8 @@ class TestSubmit(unittest.TestCase):
                 '--thread-count=0',
                 "--enable-reuse",
                 "--collection-cache-size=256",
-                '--output-name=Output from workflow secret_wf.cwl'
-                '--debug',
+                "--output-name=Output from workflow secret_wf.cwl",
+                "--debug",
                 "--on-error=continue",
                 "/var/lib/cwl/workflow.json#main",
                 "/var/lib/cwl/cwl.input.json"
@@ -1187,62 +1130,23 @@ class TestSubmit(unittest.TestCase):
                 "/var/lib/cwl/workflow.json": {
                     "content": {
                         "$graph": [
-                            {
-                                "arguments": [
-                                    "md5sum",
-                                    "example.conf"
-                                ],
-                                "class": "CommandLineTool",
-                                "hints": [
-                                    {
-                                        "class": "http://commonwl.org/cwltool#Secrets",
-                                        "secrets": [
-                                            "#secret_job.cwl/pw"
-                                        ]
-                                    }
-                                ],
-                                "id": "#secret_job.cwl",
-                                "inputs": [
-                                    {
-                                        "id": "#secret_job.cwl/pw",
-                                        "type": "string"
-                                    }
-                                ],
-                                "outputs": [
-                                    {
-                                        "id": "#secret_job.cwl/out",
-                                        "type": "File",
-                                        "outputBinding": {
-                                              "glob": "hashed_example.txt"
-                                        }
-                                    }
-                                ],
-                                "stdout": "hashed_example.txt",
-                                "requirements": [
-                                    {
-                                        "class": "InitialWorkDirRequirement",
-                                        "listing": [
-                                            {
-                                                "entry": "username: user\npassword: $(inputs.pw)\n",
-                                                "entryname": "example.conf"
-                                            }
-                                        ]
-                                    }
-                                ]
-                            },
                             {
                                 "class": "Workflow",
                                 "hints": [
                                     {
-                                        "class": "DockerRequirement",
-                                        "dockerPull": "debian:buster-slim",
-                                        "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
+                                    "class": "DockerRequirement",
+                                    "dockerPull": "debian:buster-slim",
+                                    "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
                                     },
                                     {
                                         "class": "http://commonwl.org/cwltool#Secrets",
                                         "secrets": [
                                             "#main/pw"
                                         ]
+                                    },
+                                    {
+                                        "acrContainerImage": "999999999999999999999999999999d3+99",
+                                        "class": "http://arvados.org/cwl#WorkflowRunnerResources"
                                     }
                                 ],
                                 "id": "#main",
@@ -1255,31 +1159,34 @@ class TestSubmit(unittest.TestCase):
                                 "outputs": [
                                     {
                                         "id": "#main/out",
-                                        "outputSource": "#main/step1/out",
+                                        "outputSource": "#main/step/out",
                                         "type": "File"
                                     }
                                 ],
+                                "requirements": [
+                                    {
+                                        "class": "SubworkflowFeatureRequirement"
+                                    }
+                                ],
                                 "steps": [
                                     {
-                                        "id": "#main/step1",
+                                        "id": "#main/secret_wf.cwl",
                                         "in": [
                                             {
-                                                "id": "#main/step1/pw",
+                                                "id": "#main/step/pw",
                                                 "source": "#main/pw"
                                             }
                                         ],
+                                        "label": "secret_wf.cwl",
                                         "out": [
-                                            "#main/step1/out"
+                                            {"id": "#main/step/out"}
                                         ],
-                                        "run": "#secret_job.cwl"
+                                        "run": "keep:7628e49da34b93de9f4baf08a6212817+247/secret_wf.cwl"
                                     }
                                 ]
                             }
                         ],
-                        "$namespaces": {
-                            "cwltool": "http://commonwl.org/cwltool#"
-                        },
-                        "cwlVersion": "v1.0"
+                        "cwlVersion": "v1.2"
                     },
                     "kind": "json"
                 },
@@ -1318,7 +1225,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_request_uuid(self, stubs):
         stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
         stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
@@ -1340,7 +1247,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_container_cluster_id(self, stubs):
         stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
 
@@ -1357,7 +1264,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_validate_cluster_id(self, stubs):
         stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
         exited = arvados_cwl.main(
@@ -1366,7 +1273,7 @@ class TestSubmit(unittest.TestCase):
             stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
         self.assertEqual(exited, 1)
 
-    @stubs
+    @stubs()
     def test_submit_validate_project_uuid(self, stubs):
         # Fails with bad cluster prefix
         exited = arvados_cwl.main(
@@ -1392,7 +1299,7 @@ class TestSubmit(unittest.TestCase):
 
 
     @mock.patch("arvados.collection.CollectionReader")
-    @stubs
+    @stubs()
     def test_submit_uuid_inputs(self, stubs, collectionReader):
         collectionReader().exists.return_value = True
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
@@ -1406,6 +1313,7 @@ class TestSubmit(unittest.TestCase):
                 m.execute.return_value = {"items": []}
             return m
         stubs.api.collections().list.side_effect = list_side_effect
+        collectionReader().portable_data_hash.return_value = "99999999999999999999999999999998+99"
 
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug",
@@ -1427,7 +1335,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_mismatched_uuid_inputs(self, stubs):
         def list_side_effect(**kwargs):
             m = mock.MagicMock()
@@ -1460,7 +1368,7 @@ class TestSubmit(unittest.TestCase):
                 cwltool_logger.removeHandler(stderr_logger)
 
     @mock.patch("arvados.collection.CollectionReader")
-    @stubs
+    @stubs()
     def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
         capture_stderr = StringIO()
@@ -1491,7 +1399,7 @@ class TestSubmit(unittest.TestCase):
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
 
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
             {
                 "class": "http://arvados.org/cwl#ProcessProperties",
                 "processProperties": [
@@ -1506,11 +1414,17 @@ class TestSubmit(unittest.TestCase):
                      }
                     }
                 ],
+            },
+            {
+                "acrContainerImage": "999999999999999999999999999999d3+99",
+                "class": "http://arvados.org/cwl#WorkflowRunnerResources"
             }
         ]
-        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
-            "arv": "http://arvados.org/cwl#"
-        }
+        #expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
+        #    "arv": "http://arvados.org/cwl#"
+        #}
+
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:df44f9dd4b9467159f210f967e45417f+312/wf/submit_wf_process_properties.cwl"
 
         expect_container["properties"].update({
             "baz": "blorp.txt",
@@ -1528,7 +1442,7 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_submit_enable_preemptible(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
@@ -1537,11 +1451,13 @@ class TestSubmit(unittest.TestCase):
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate', '--disable-color',
-                        '--eval-timeout=20', '--thread-count=0',
-                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug', '--on-error=continue',
                                        '--enable-preemptible',
-                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -1549,7 +1465,7 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_submit_disable_preemptible(self, stubs):
         exited = arvados_cwl.main(
             ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
@@ -1558,11 +1474,57 @@ class TestSubmit(unittest.TestCase):
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
-                        '--no-log-timestamps', '--disable-validate', '--disable-color',
-                        '--eval-timeout=20', '--thread-count=0',
-                        '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug', '--on-error=continue',
                                        '--disable-preemptible',
-                        '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
+    @stubs()
+    def test_submit_container_prefer_cached_downloads(self, stubs):
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--prefer-cached-downloads",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug', "--on-error=continue", '--prefer-cached-downloads',
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(stubs.capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
+    @stubs()
+    def test_submit_container_varying_url_params(self, stubs):
+        exited = arvados_cwl.main(
+            ["--submit", "--no-wait", "--api=containers", "--debug", "--varying-url-params", "KeyId,Signature",
+                "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+                                       '--no-log-timestamps', '--disable-validate', '--disable-color',
+                                       '--eval-timeout=20', '--thread-count=0',
+                                       '--enable-reuse', "--collection-cache-size=256",
+                                       '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+                                       '--debug', "--on-error=continue", "--varying-url-params=KeyId,Signature",
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))
@@ -1574,11 +1536,13 @@ class TestSubmit(unittest.TestCase):
 class TestCreateWorkflow(unittest.TestCase):
     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
     expect_workflow = StripYAMLComments(
-        open("tests/wf/expect_upload_packed.cwl").read().rstrip())
+        open("tests/wf/expect_upload_wrapper.cwl").read().rstrip())
+    expect_workflow_altname = StripYAMLComments(
+        open("tests/wf/expect_upload_wrapper_altname.cwl").read().rstrip())
 
     def setUp(self):
         cwltool.process._names = set()
-        arvados_cwl.arvdocker.arv_docker_clear_cache()
+        #arvados_cwl.arvdocker.arv_docker_clear_cache()
 
     def tearDown(self):
         root_logger = logging.getLogger('')
@@ -1587,7 +1551,7 @@ class TestCreateWorkflow(unittest.TestCase):
         handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
         root_logger.handlers = handlers
 
-    @stubs
+    @stubs()
     def test_create(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1596,6 +1560,7 @@ class TestCreateWorkflow(unittest.TestCase):
             ["--create-workflow", "--debug",
              "--api=containers",
              "--project-uuid", project_uuid,
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1617,7 +1582,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_name(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1627,6 +1592,7 @@ class TestCreateWorkflow(unittest.TestCase):
              "--api=containers",
              "--project-uuid", project_uuid,
              "--name", "testing 123",
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1638,7 +1604,7 @@ class TestCreateWorkflow(unittest.TestCase):
                 "owner_uuid": project_uuid,
                 "name": "testing 123",
                 "description": "",
-                "definition": self.expect_workflow,
+                "definition": self.expect_workflow_altname,
             }
         }
         stubs.api.workflows().create.assert_called_with(
@@ -1649,7 +1615,7 @@ class TestCreateWorkflow(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_update(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
@@ -1657,6 +1623,7 @@ class TestCreateWorkflow(unittest.TestCase):
         exited = arvados_cwl.main(
             ["--update-workflow", self.existing_workflow_uuid,
              "--debug",
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1676,7 +1643,7 @@ class TestCreateWorkflow(unittest.TestCase):
         self.assertEqual(exited, 0)
 
 
-    @stubs
+    @stubs()
     def test_update_name(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
@@ -1684,6 +1651,7 @@ class TestCreateWorkflow(unittest.TestCase):
         exited = arvados_cwl.main(
             ["--update-workflow", self.existing_workflow_uuid,
              "--debug", "--name", "testing 123",
+             "--disable-git",
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
@@ -1691,7 +1659,7 @@ class TestCreateWorkflow(unittest.TestCase):
             "workflow": {
                 "name": "testing 123",
                 "description": "",
-                "definition": self.expect_workflow,
+                "definition": self.expect_workflow_altname,
                 "owner_uuid": project_uuid
             }
         }
@@ -1702,7 +1670,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          self.existing_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_collection_per_tool(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1711,10 +1679,11 @@ class TestCreateWorkflow(unittest.TestCase):
             ["--create-workflow", "--debug",
              "--api=containers",
              "--project-uuid", project_uuid,
+             "--disable-git",
              "tests/collection_per_tool/collection_per_tool.cwl"],
             stubs.capture_stdout, sys.stderr, api_client=stubs.api)
 
-        toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+        toolfile = "tests/collection_per_tool/collection_per_tool_wrapper.cwl"
         expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
 
         body = {
@@ -1732,7 +1701,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_with_imports(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}
@@ -1751,7 +1720,7 @@ class TestCreateWorkflow(unittest.TestCase):
                          stubs.expect_workflow_uuid + '\n')
         self.assertEqual(exited, 0)
 
-    @stubs
+    @stubs()
     def test_create_with_no_input(self, stubs):
         project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
         stubs.api.groups().get().execute.return_value = {"group_class": "project"}